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Displaying Results 201 - 225 of 2088 on page 9 of 84
Marked
Mark
Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines
(2006)
Keane, Thomas; Page, Andrew; Naughton, Thomas J.; Travers, Simon; McInerney, James
Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines
(2006)
Keane, Thomas; Page, Andrew; Naughton, Thomas J.; Travers, Simon; McInerney, James
Abstract:
Abstract Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computational requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse-grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efficiency tests that show how to maximise efficiency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.nuim.ie/distributed.
http://mural.maynoothuniversity.ie/917/
Marked
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Molecular evidence for dim-light vision in the last common ancestor of the vertebrates
(2006)
Pisani, Davide; Mohun, Samantha; Harris, Simon; McInerney, James; Wilkinson, Mark
Molecular evidence for dim-light vision in the last common ancestor of the vertebrates
(2006)
Pisani, Davide; Mohun, Samantha; Harris, Simon; McInerney, James; Wilkinson, Mark
Abstract:
Animal vision is mediated through pigments belonging exclusively to the opsin family. These are members of the G-protein-coupled receptor family that bind retinal [1]. Based on function and phylogenetic relationship, vertebrate visual opsins can be clustered in five groups: Rhod photoreceptors (Rh1), Rh1-like (Rh2), Short Wave Sensitive (SWS1), SWS1-like (SWS2), and Long (LWS) or Medium (MWS) Wave Length Sensitive (LWS/MWS). Rh1 is used for seeing under dim light conditions (scotopic vision), while the others permit full colour (photopic) vision in bright light 2, 3, 4 and 5. Opsins have diversified by a series of gene duplications, and the inferred order of these duplications indicates that photopic vision predated scotopic vision in vertebrates 2, 3, 4 and 5.
http://mural.maynoothuniversity.ie/919/
Marked
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Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
(2006)
Keane, Thomas; Creevey, Christopher; Pentony, Melissa; Naughton, Thomas J.; McInerney, ...
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
(2006)
Keane, Thomas; Creevey, Christopher; Pentony, Melissa; Naughton, Thomas J.; McInerney, James
Abstract:
Background In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. Results We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistic...
http://mural.maynoothuniversity.ie/916/
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The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa
(2005)
Philip, Gayle K.; Creevey, Christopher J.; McInerney, James O.
The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa
(2005)
Philip, Gayle K.; Creevey, Christopher J.; McInerney, James O.
Abstract:
In considering the best possible solutions for answering phylogenetic questions from genomic sequences, we have chosen a strategy that we suggest is superior to others that have gone previously. We have ignored multigene families and instead have used single-gene families. This minimizes the inadvertent analysis of paralogs. We have employed strict data controls and have reasoned that if a protein is not capable of recovering the uncontroversial parts of a phylogenetic tree, then why should we use it for the more controversial parts? We have sliced and diced the data in as many ways as possible in order to uncover the signals in that data. Using this strategy, we have tested two controversial hypotheses concerning eukaryotic phylogenetic relationships: the placement of arthropoda and nematodes and the relationships of animals, plants, and fungi. We have constructed phylogenetic trees from 780 single-gene families from 10 completed genomes and amalgamated these into a single supertre...
http://mural.maynoothuniversity.ie/673/
Marked
Mark
Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales
(2006)
Fitzpatrick, David A.; Creevey, Christopher J.; McInerney, James O.
Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales
(2006)
Fitzpatrick, David A.; Creevey, Christopher J.; McInerney, James O.
Abstract:
Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible a-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the a-proteobacteria, but it appears to be restricted to a minority of genes (;23%) most of whom (;74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement o...
http://mural.maynoothuniversity.ie/668/
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An Insight into the Impact of Arable Farming on Irish Biodiversity: A Scarcity of Studies Hinders a Rigorous Assessment
(2008)
O'Brien, Martin; Spillane, Charles; Meade, Conor; Mullins, Ewen
An Insight into the Impact of Arable Farming on Irish Biodiversity: A Scarcity of Studies Hinders a Rigorous Assessment
(2008)
O'Brien, Martin; Spillane, Charles; Meade, Conor; Mullins, Ewen
Abstract:
To help understand and counteract future agronomic challenges to farmland biodiversity, it is essential to know how present farming practices have affected biodiversity on Irish farms. We present an overview of existing research data and conclusions, describing the impact of crop cultivation on biodiversity on Irish arable farms. An extensive literature review clearly indicates that peer-reviewed publications on research conducted in Ireland on this topic are quite scarce: just 21 papers investigating the effect of conventional crop cultivation on Irish biodiversity have been published within the past 30 years. Principally, these studies have concluded that conventional crop cultivation has had an adverse impact on biodiversity on Irish farms, with 15 of the 21 studies demonstrating negative trends for the taxa investigated. Compared to other EU states, the relative dearth of baseline data and absence of monitoring programmes designed to assess the specific impacts of crop cultivati...
http://mural.maynoothuniversity.ie/3545/
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The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)
(2005)
Shannon, Adam J.; Browne, John A.; Boyd, Jacqueline; Fitzpatrick, David A.; Burnell, Ann
The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)
(2005)
Shannon, Adam J.; Browne, John A.; Boyd, Jacqueline; Fitzpatrick, David A.; Burnell, Ann
Abstract:
Members of the genus Panagrolaimus are bacterialfeeding nematodes that occupy a diversity of niches ranging from Antarctic and temperate soils to terrestrial mosses. Some members of this genus are able to survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. We have assembled a collection of Panagrolaimus species and strains and have investigated their anhydrobiotic phenotypes. Our data show that within the genus Panagrolaimus there is a continuum of strains ranging from those unable to survive exposure to low relative humidity (RH) without prior preconditioning at high RH (slow desiccation strategists), through strains that have limited ability to survive rapid desiccation but whose anhydrobiotic ability improves upon preconditioning, to strains such as P. superbus that can readily survive immediate exposure to severe desiccation (fast desiccation strategists). Using this panel of nematodes we investigated the effect of preincubation at...
http://mural.maynoothuniversity.ie/517/
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Does a tree-like phylogeny only exist at the tips in the prokaryotes?
(2004)
Creevey, Christopher J.; Fitzpatrick, David A.; Philip, Gayle K.; Kinsella, Rhoda J.; O...
Does a tree-like phylogeny only exist at the tips in the prokaryotes?
(2004)
Creevey, Christopher J.; Fitzpatrick, David A.; Philip, Gayle K.; Kinsella, Rhoda J.; O'Connell, Mary J.; Pentony, Melissa M.; Travers, Simon A.; Wilkinson, Mark; McInerney, James O.
Abstract:
The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent c-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in c-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny...
http://mural.maynoothuniversity.ie/414/
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Some Desiderata for Liberal Supertrees
(2004)
Wilkinson, Mark; Thorley, Joseph L.; Pisani, Davide; Lapointe, Francois-Joseph; McInern...
Some Desiderata for Liberal Supertrees
(2004)
Wilkinson, Mark; Thorley, Joseph L.; Pisani, Davide; Lapointe, Francois-Joseph; McInerney, James O.
Abstract:
Although a variety of supertree methods has been proposed, our understanding of these methods is limited. In turn, this limits the potential for biologists who seek to construct supertrees to make informed choices among the available methods. In this chapter we distinguish between supertree methods that offer a conservative synthesis of the relationships that are agreed upon or uncontradicted by all the input trees and liberal supertree methods which have the potential to resolve conflict. We list a series of potential desiderata (i.e.desirable properties) of liberal supertree methods, discuss their relevance to biologists and highlight where it is known that particular methods do or do not satisfy them. For biologists, the primary aim of liberal supertree construction is to produce accurate phylogenies and most of our desiderata relate to this prime objective. Secondary desiderata pertain to the practicality of supertree methods, particularly their speed.
http://mural.maynoothuniversity.ie/411/
Marked
Mark
Identification, cloning, and functional expression of three glutathione transferase genes from Aspergillus fumigatus
(2005)
Burns, Claire; Geraghty, Rachel; Neville, Claire; Murphy, Alan; Kavanagh, Kevin; Doyle,...
Identification, cloning, and functional expression of three glutathione transferase genes from Aspergillus fumigatus
(2005)
Burns, Claire; Geraghty, Rachel; Neville, Claire; Murphy, Alan; Kavanagh, Kevin; Doyle, Sean
Abstract:
Analysis of the genome of the human pathogen, Aspergillus fumigatus, revealed the presence of several putative glutathione transferase (GST) open reading frames. Three A. fumigatus GST genes, termed gstA, B, and C, were cloned and recombinant proteins expressed in Escherichia coli. Functional analysis of recombinant gstA–C conWrms that the enzymes exhibit GST activity and glutathione peroxidase activity. RT-PCR conWrmed low basal expression of gstA and gstC which was markedly up-regulated (at least 4£– 10£) in the presence of either H2O2 or 1-chloro-2,4-dinitrobenzene (CDNB). GstB expression was only observed in the presence of CDNB. These results demonstrate for the Wrst time the existence of three functional GSTs in A. fumigatus and strongly suggest a role for these enzymes in the response of the organism to both oxidative stress and xenobiotic presence.
http://mural.maynoothuniversity.ie/230/
Marked
Mark
Heterorhabditis, Steinernema and their bacterial symbionts - lethal pathogens of insects
(2000)
Burnell, Ann; Stock, S. Patricia
Heterorhabditis, Steinernema and their bacterial symbionts - lethal pathogens of insects
(2000)
Burnell, Ann; Stock, S. Patricia
Abstract:
The entomopathogenic nematodes (EPN) Heterorhabditis and Steinernema together with their symbiont bacteria Photorhabdus and Xenorhabdus, respectively, are obligate and lethal parasites of insects. EPN can provide effective biological control of some important lepidopteran, dipteran and coleopteran pests of commercial crops and they are amenable to large-scale culture in liquid fermentors. They are unique among rhabditids in having a symbiotic relationshipwith an enteric bacterium species. The bacterial symbiont is required to kill the insect host and to digest the host tissues, thereby providing suitable nutrient conditions for nematode growth and development. This review describes the general biology of EPN and their symbionts and gives an overview of studies to date on EPN biodiversity, biogeography and phylogeny. The impetus for research in EPN and their symbionts has come about because of their biological control potential, with much of the focus in EPN research having been on a...
http://mural.maynoothuniversity.ie/177/
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Transition from Natively Unfolded to Folded State Induced by Desiccation in an Anhydrobiotic Nematode Protein
(2003)
Goyal, Kshamata; Tisi, Laurence; Basran, Amrik; Browne, John; Burnell, Ann; Zurdo, Jesu...
Transition from Natively Unfolded to Folded State Induced by Desiccation in an Anhydrobiotic Nematode Protein
(2003)
Goyal, Kshamata; Tisi, Laurence; Basran, Amrik; Browne, John; Burnell, Ann; Zurdo, Jesus; Tunnacliffe, Alan
Abstract:
Late embryogenesis abundant (LEA) proteins are associated with desiccation tolerance in resurrection plants and in plant seeds, and the recent discovery of a dehydration- induced Group 3 LEA-like gene in the nematode Aphelenchus avenae suggests a similar association in anhydrobiotic animals. Despite their importance, little is known about the structure of Group 3 LEA proteins, although computer modeling and secondary structure algorithms predict a largely -helical monomer that forms coiled coil oligomers. We have therefore investigated the structure of the nematode protein, AavLEA1, in the first such analysis of a well characterized Group 3 LEA-like protein. Immunoblotting and subunit cross-linking experiments demonstrate limited oligomerization of AavLEA1, but analytical ultracentrifugation and gel filtration show that the vast majority of the protein is monomeric. Moreover, CD, fluorescence emission, and Fourier transform-infrared spectroscopy indicate an unstructured conformation...
http://mural.maynoothuniversity.ie/172/
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The Velvet Family of Fungal Regulators Contains a DNA-Binding Domain Structurally Similar to NF-kB
(2013)
Ahmed, Yasar Luqman; Gerke, Jennifer; Park, Hee-Soo; Bayram, Ozgur; Neumann, Piotr; Ni,...
The Velvet Family of Fungal Regulators Contains a DNA-Binding Domain Structurally Similar to NF-kB
(2013)
Ahmed, Yasar Luqman; Gerke, Jennifer; Park, Hee-Soo; Bayram, Ozgur; Neumann, Piotr; Ni, Min; Dickmanns, Achim; Kim, Sun Chang; Yu, Jae-Hyuk; Braus, Gerhard H.; Ficner, Ralf
Abstract:
Morphological development of fungi and their combined production of secondary metabolites are both acting in defence and protection. These processes are mainly coordinated by velvet regulators, which contain a yet functionally and structurally uncharacterized velvet domain. Here we demonstrate that the velvet domain of VosA is a novel DNA-binding motif that specifically recognizes an 11-nucleotide consensus sequence consisting of two motifs in the promoters of key developmental regulatory genes. The crystal structure analysis of the VosA velvet domain revealed an unforeseen structural similarity with the Rel homology domain (RHD) of the mammalian transcription factor NF-kB. Based on this structural similarity several conserved amino acid residues present in all velvet domains have been identified and shown to be essential for the DNA binding ability of VosA. The velvet domain is also involved in dimer formation as seen in the solved crystal structures of the VosA homodimer and the V...
http://mural.maynoothuniversity.ie/6242/
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The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
(2008)
McCann, Angela; Cotton, James A.; McInerney, James O.
The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
(2008)
McCann, Angela; Cotton, James A.; McInerney, James O.
Abstract:
Background: In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present. Results: We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are sign...
http://mural.maynoothuniversity.ie/6263/
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Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
(2012)
Wuest, Samuel E.; Ó'Maoiléidigh, Diarmuid S.; Rae, Liina; Kwasniewska, Kamila; Rag...
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
(2012)
Wuest, Samuel E.; Ó'Maoiléidigh, Diarmuid S.; Rae, Liina; Kwasniewska, Kamila; Raganelli, Andrea; Hanczaryka, Katarzyna; Lohan, Amanda J.; Loftus, Brendan; Graciet, Emmanuelle; Wellmer, Frank
Abstract:
How different organs are formed from small sets of undifferentiated precursor cells is a key question in developmental biology. To understand the molecular mechanisms underlying organ specification in plants, we studied the function of the homeotic selector genes APETALA3 (AP3) and PISTILLATA (PI), which control the formation of petals and stamens during Arabidopsis flower development. To this end, we characterized the activities of the transcription factors that AP3 and PI encode throughout flower development by using perturbation assays as well as transcript profiling and genomewide localization studies, in combination with a floral induction system that allows a stage-specific analysis of flower development by genomic technologies. We discovered considerable spatial and temporal differences in the requirement for AP3/PI activity during flower formation and show that they control different sets of genes at distinct phases of flower development. The genomewide identification of tar...
http://mural.maynoothuniversity.ie/6264/
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Deletion and Allelic Exchange of the Aspergillus fumigatus veA Locus via a Novel Recyclable Marker Module
(2005)
Krappman, Sven; Bayram, Ozgur; Braus, Gerhard H.
Deletion and Allelic Exchange of the Aspergillus fumigatus veA Locus via a Novel Recyclable Marker Module
(2005)
Krappman, Sven; Bayram, Ozgur; Braus, Gerhard H.
Abstract:
Detailed evaluation of gene functions in an asexual fungus requires advanced methods of molecular biology. For the generation of targeted gene deletions in the opportunistic pathogen Aspergillus fumigatus we designed a novel blaster module allowing dominant selection of transformants due to resistance to phleomycin as well as dominant (counter)selection of a Cre recombinase-mediated marker excision event. For validation purposes we have deleted the A. fumigatus pabaA gene in a wild-type isolate by making use of this cassette. The resulting pabaA::loxP strain served as the recipient for subsequent targeting of the velvet locus. Homologous reconstitution of the deleted gene was performed by an allele whose expression is driven in a nitrogen source-dependent manner, as validated by Northern analyses. Overexpression of the veA locus in A. fumigatus does not result in any obvious phenotype, whereas the sporulation capacities of the veA null mutant are reduced on nitratecontaining medium,...
http://mural.maynoothuniversity.ie/6249/
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A Delineation of Mesenchymal Stromal Cell Therapeutic Action in New Models of Acute and Chronic Graft versus Host Disease
(2015)
Healy, Marc E.
A Delineation of Mesenchymal Stromal Cell Therapeutic Action in New Models of Acute and Chronic Graft versus Host Disease
(2015)
Healy, Marc E.
Abstract:
The potent immune regulatory capacity of mesenchymal stromal cells (MSC) has been extensively characterised in terms of T cells, natural killer cells and dendritic cells suppression; however the ability of MSC to modulate B cell biology is not fully understood. This immune suppressive ability has led to the development of MSC therapy for the treatment of inflammatory and auto-immune disease, and has already demonstrated beneficial effects during GvHD and Crohn’s disease. However, the mechanisms employed by MSC therapy to modulate disease progression have not been identified. The key goals for this thesis were (1) to determine how MSC effect B cell function and to identify the mechanisms by which this effect is mediated, and (2) the development of novel mouse models of chronic and acute GvHD to elucidate the mechanism of action by which MSC attenuate disease progression. This study demonstrated than MSC support the activation, proliferation and survival of human CD19+ peripheral B ce...
http://mural.maynoothuniversity.ie/6035/
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Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa
(2009)
Sperling, Erik A.; Peterson, Devin J.; Pisani, Davide
Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa
(2009)
Sperling, Erik A.; Peterson, Devin J.; Pisani, Davide
Abstract:
The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using di...
http://mural.maynoothuniversity.ie/3793/
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Mark
Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris
(2011)
Colgan, Thomas J.; Carolan, James C.; Bridgett, Stephen J.; Sumner, Seirian; Blaxter, M...
Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris
(2011)
Colgan, Thomas J.; Carolan, James C.; Bridgett, Stephen J.; Sumner, Seirian; Blaxter, Mark L.; Brown, Mark J.F.
Abstract:
Background: Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism has been key to the evolution of the Hymenoptera, and particularly the social Hymenoptera where the genome of a single species regulates distinct larval stages, sexual dimorphism and physical castes within the female sex. Transcriptomic analyses of social Hymenoptera will therefore provide unique insights into how changes in gene expression underlie such complexity. Here we describe gene expression in individual specimens of the pre-adult stages, sexes and castes of the key pollinator, the buff-tailed bumblebee Bombus terrestris. Results: cDNA was prepared from mRNA from five life cycle stages (one larva, one pupa, one male, one gyne and two workers) and a total of 1,610,742 expressed sequence tags (ESTs) were generated using Roche 454 technology, substantially inc...
http://mural.maynoothuniversity.ie/3784/
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Mark
NFκB2 p52 has a role in antiviral immunity through IKKε -dependent induction of Sp1 and IL-15
(2013)
Doyle, Sarah L.; Shirey, Kari Ann; McGettrick, Anne F.; Kenny, Elaine F.; Carpenter, Su...
NFκB2 p52 has a role in antiviral immunity through IKKε -dependent induction of Sp1 and IL-15
(2013)
Doyle, Sarah L.; Shirey, Kari Ann; McGettrick, Anne F.; Kenny, Elaine F.; Carpenter, Susan B.; Caffrey, Brian E.; Gardan, Siobhan; Quinn, Susan R.; Cammano, Jorge H.; Moynagh, Paul N.; Vogel, Stefani N.; O'Neill, Luke A.
Abstract:
In this study we describe a previously unreported function for NFκB2, an NFκB family transcription factor, in antiviral immunity. NFκB2 is induced in response to Poly(I:C), a mimic of viral dsRNA. Poly(I:C), acting via TLR3, induces p52- dependent transactivation of a reporter gene in a manner that requires the kinase activity of IKKε and the transactivating potential of RelA/p65. We identify a novel NFκB2 binding site in the promoter of the transcription factor Sp1 which is required for Sp1 gene transcription activated by Poly(I:C). We show that Sp1 is required for IL-15 induction by both Poly(I:C) and Respiratory Syncitial Virus, a response that also requires NFκB2 and IKKε. Our study identifies NFκB2 as a target for IKKε in anti -viral immunity and describes, for the first time, a role for NFκB2 in the regulation of gene expression in response to viral infection.
http://mural.maynoothuniversity.ie/4967/
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Mark
Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae
(2010)
Reardon, Wesley; Chakrabortee, Sohini; Pereira, Tiago Campos; Tyson, Trevor; Banton, Ma...
Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae
(2010)
Reardon, Wesley; Chakrabortee, Sohini; Pereira, Tiago Campos; Tyson, Trevor; Banton, Matthew C.; Dolan, Katharine M.; Culleton, Bridget A.; Wise, Michael J.; Burnell, Ann; Tunnacliffe, Alan
Abstract:
Background: Some organisms can survive extreme desiccation by entering a state of suspended animation known as anhydrobiosis. The free-living mycophagous nematode Aphelenchus avenae can be induced to enter anhydrobiosis by pre-exposure to moderate reductions in relative humidity (RH) prior to extreme desiccation. This preconditioning phase is thought to allow modification of the transcriptome by activation of genes required for desiccation tolerance. Results: To identify such genes, a panel of expressed sequence tags (ESTs) enriched for sequences upregulated in A. avenae during preconditioning was created. A subset of 30 genes with significant matches in databases, together with a number of apparently novel sequences, were chosen for further study. Several of the recognisable genes are associated with water stress, encoding, for example, two new hydrophilic proteins related to the late embryogenesis abundant (LEA) protein family. Expression studies confirmed EST panel members to be ...
http://mural.maynoothuniversity.ie/2644/
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Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
(2013)
Xu, Linan; Hasin, Naushaba; Shen, Manli; He, Jianwei; Xue, Youlin; Zhou, Xiaohong; Perr...
Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
(2013)
Xu, Linan; Hasin, Naushaba; Shen, Manli; He, Jianwei; Xue, Youlin; Zhou, Xiaohong; Perrett, Sarah; Song, Youtao; Jones, Gary W.
Abstract:
Genetic screens using Saccharomyces cerevisiae have identified an array of cytosolic Hsp70 mutants that are impaired in the ability to propagate the yeast [PSI+] prion. The best characterized of these mutants is the Ssa1 L483W mutant (so-called SSA1-21), which is located in the substrate-binding domain of the protein. However, biochemical analysis of some of these Hsp70 mutants has so far failed to provide major insight into the specific functional changes in Hsp70 that cause prion impairment. In order to gain a better understanding of the mechanism of Hsp70 impairment of prions we have taken an in silico approach and focused on the Escherichia coli Hsp70 ortholog DnaK. Using steered molecular dynamics simulations (SMD) we demonstrate that DnaK variant L484W (analogous to SSA1-21) is predicted to bind substrate more avidly than wild-type DnaK due to an increase in numbers of hydrogen bonds and hydrophobic interactions between chaperone and peptide. Additionally the presence of the l...
http://mural.maynoothuniversity.ie/4297/
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Review: Comparison's Chimeras: Sandra Bamford. Biology Unmoored: Melanesian Reflections on Life and Biotechnology. Berkeley: University of California Press, 2007. 230 pp.
(2008)
Strong, Thomas
Review: Comparison's Chimeras: Sandra Bamford. Biology Unmoored: Melanesian Reflections on Life and Biotechnology. Berkeley: University of California Press, 2007. 230 pp.
(2008)
Strong, Thomas
Abstract:
Abstract included in text.
http://mural.maynoothuniversity.ie/4263/
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The Synthetic Cannabinoid R(+)WIN55,212-2 Augments Interferon-β Expression via Peroxisome Proliferator-activated Receptor-α
(2012)
Downer, Eric J.; Clifford, Eileen; Amu, Sylvie; Fallon, Padraic G.; Moynagh, Paul N.
The Synthetic Cannabinoid R(+)WIN55,212-2 Augments Interferon-β Expression via Peroxisome Proliferator-activated Receptor-α
(2012)
Downer, Eric J.; Clifford, Eileen; Amu, Sylvie; Fallon, Padraic G.; Moynagh, Paul N.
Abstract:
We have demonstrated that R()WIN55,212-2, a synthetic cannabinoid that possesses cannabimimetic properties, acts as a novel regulator of Toll-like receptor 3 (TLR3) signaling to interferon (IFN) regulatory factor 3 (IRF3) activation and IFN- expression, and this is critical for manifesting its protective effects in a murine multiple sclerosis model. Here we investigated the role of peroxisome proliferator-activated receptor- (PPAR) in mediating the effects of R()WIN55,212-2 on this pathway. Data herein demonstrate that the TLR3 agonist poly(I:C) promotes IFN- expression and R()WIN55,212-2 enhances TLR3-induced IFN- expression in a stereoselective manner via PPAR. R()WIN55,212-2 promotes increased transactivation and expression of PPAR. Using the PPAR antagonist GW6471, we demonstrate that R()WIN55,212-2 acts via PPAR to activate JNK, activator protein-1, and positive regulatory domain IV to transcriptionally regulate the IFN- promoter. Furthermore, GW6471 ameliorated the protective ...
http://mural.maynoothuniversity.ie/4266/
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Identification of the Synthetic Cannabinoid R()WIN55,212-2 as a Novel Regulator of IFN Regulatory Factor 3 Activation and IFN- Expression
(2011)
Downer, Eric J.; Clifford, Eileen; Gran, Bruno; Hendrik, J. Nel; Fallon, Padraig G.; Mo...
Identification of the Synthetic Cannabinoid R()WIN55,212-2 as a Novel Regulator of IFN Regulatory Factor 3 Activation and IFN- Expression
(2011)
Downer, Eric J.; Clifford, Eileen; Gran, Bruno; Hendrik, J. Nel; Fallon, Padraig G.; Moynagh, Paul N.
Abstract:
Beta Interferons (IFN-βs) represent one of the first line treatments for relapsing remitting multiple sclerosis (RRMS), slowing disease progression whilst reducing the frequency of relapses. Despite this, more effective, well tolerated therapeutic strategies are needed. Cannabinoids palliate experimental autoimmune encephalomyelitis (EAE) symptoms and have therapeutic potential in MS patients although the precise molecular mechanism for these effects is not understood. Toll-like receptor (TLR) signaling controls innate immune responses and TLRs are implicated in MS. Here we demonstrate that the synthetic cannabinoid R(+)WIN55,212-2 is a novel regulator of TLR3 and TLR4 signaling by inhibiting the pro-inflammatory signaling axis triggered by TLR3 and TLR4 whilst selectively augmenting TLR3-induced activation of IFN regulatory factor 3 (IRF3) and expression of IFN-β. We present evidence that R(+)WIN55,212-2 strongly promotes the nuclear localization of IRF3. The potentiation of IFN-β ...
http://mural.maynoothuniversity.ie/4267/
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